Cas12a combinatorial knockout screens map genetic interaction network of DNA damage response

Researchers have used Cas12a-based combinatorial knockout screens to interrogate the functional architecture of the DNA damage response (DDR), a network of cellular pathways that maintains genome integrity when DNA is damaged. The preprint, posted to bioRxiv, describes the systematic disruption of 233 DDR genes — selected because they are frequently mutated in cancer and other genetic diseases — either individually or in pairwise combinations, generating data on more than 27,000 gene-pair interactions under normal cell-growth conditions.

The approach exploits Cas12a's ability to process multiple guide RNAs from a single transcript, making high-throughput combinatorial perturbation more tractable than with standard Cas9 systems. By comparing phenotypic outcomes of single versus double knockouts, the study aims to distinguish between genes that act redundantly, synergistically, or antagonistically within DDR pathways.

The resulting genetic interaction map is intended as a resource for understanding which combinations of DDR gene disruptions are lethal or growth-impairing — information relevant to identifying potential therapeutic vulnerabilities in tumour cells that already carry somatic DDR mutations. The authors note that the screen was conducted under unperturbed conditions; how interactions shift under genotoxic stress remains to be characterised.

This work has not yet been peer-reviewed. The data resource it describes could inform future experimental and computational analyses of DDR pathway organisation in cancer biology.